| Package | Maintainer | Title |
|---|---|---|
| affycoretools | James W. MacDonald | Functions useful for those doing repetitive analyses with Affymetrix GeneChips. |
| attract | Jessica Mar | Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape |
| BioNet | Marcus Dittrich | Routines for the functional analysis of biological networks |
| CoGAPS | Elana J. Fertig , Michael F. Ochs | Coordinated Gene Activity in Pattern Sets |
| ddCt | Jitao David Zhang | The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR) |
| DEGseq | Likun Wang | Identify Differentially Expressed Genes from RNA-seq data |
| eisa | Gabor Csardi | Expression data analysis via the Iterative Signature Algorithm |
| ExiMiR | Sylvain Gubian | R functions for the normalization of Exiqon miRNA array data |
| ExpressionView | Gabor Csardi | Visualize biclusters identified in gene expression data |
| farms | Djork-Arne Clevert | FARMS - Factor Analysis for Robust Microarray Summarization |
| GeneGA | Zhenpeng Li | Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm |
| goseq | Matthew Young | Gene Ontology analyser for RNA-seq and other length biased data |
| HTqPCR | Heidi Dvinge | Automated analysis of high-throughput qPCR data |
| LiquidAssociation | Yen-Yi Ho | LiquidAssociation |
| Mulcom | Claudio Isella | Calculates MulCom test |
| netresponse | Leo Lahti | NetResponse: functional network analysis |
| oligo | Benilton Carvalho | Preprocessing tools for oligonucleotide arrays. |
| pint | Olli-Pekka Huovilainen | Pairwise INTegration of functional genomics data |
| PROMISE | Xueyuan Cao | PRojection Onto the Most Interesting Statistical Evidence |
| qpcrNorm | Jessica Mar | Data-driven normalization strategies for high-throughput qPCR data. |
| qpgraph | Robert Castelo | Reverse engineering of molecular regulatory networks with qp-graphs |
| RBioinf | Robert Gentleman | RBioinf |
| RmiR | Francesco Favero | Package to work with miRNAs and miRNA targets with R |
| rnaSeqMap | Michal Okoniewski | rnaSeq analyses using xmapcore database |
| RPA | Leo Lahti | RPA: probe reliability and differential gene expression analysis |
| RTools4TB | Aurelie Bergon | Data mining of public microarray data through connections to the TranscriptomeBrowser database. |
| safe | William T. Barry | Significance Analysis of Function and Expression |
| siggenes | Holger Schwender | Multiple testing using SAM and Efron's empirical Bayes approaches |
| snm | Brig Mecham | Supervised Normalization of Microarrays |
| survcomp | Benjamin Haibe-Kains , Markus Schroeder | Performance Assessment and Comparison for Survival Analysis |
| tigre | Antti Honkela | Transcription factor Inference through Gaussian process Reconstruction of Expression |
| xps | Christian Stratowa | Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays |